This is the map of the NPC Main line as it existed at the time the NPC prototype is being loosely modeled as a freelance railroad, the Pacific Coast & Northern. The first image is from the Northeastern part of the NPC. The second is from the Southwestern part of the NPC.
In comparing these maps to the layout, you will see that the vast majority of the layout focuses on the northeastern portion of the NPC. The major exception is the shops, yards, and dock in Sausalito.